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Bioinformatics Recipes

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This course has launched on October 1st, 2018 and is part of the graduate level BMMB 852: Applied Bioinformatics course at Penn State.

Lectures and new recipes will be published on an approximately weekly schedule.

Each lecture in this course covers a specific data analysis protocol with one or more example workflows. The course is a companion to the Learn Bioinformatics in 100 hours course and the Biostar Handbook.

In addition, we have developed a new web service that allows readers to investigate the output of each of these workflows.

To see how each recipe works in practice visit the Bioinformatics Cookbook.

Lecture Tests
Recipe 1: What is a Recipe?

What is a recipe, how to use the Recipes website

Recipe 2: FASTQ Quality Control

FASTQ quality control

Recipe 4: Short Read Aligners

Aligning short reads to reference genomes

Recipe 5: Filtering SAM files

How to process alignment files

Recipe 6: Visualizing Large Scale Variation

Detecting large-scale variations

Recipe 7


Recipe 8


Recipe 9


Recipe 10